Whenever I add a new file to the games folder and let dolphin create a save game to /user/wii/title, dolphin crashes at startup game folder scanning until I delete/move the game or delete/move the savegame.

If no savegame is present, dolphin starts normally. This happens with every new game (new means it has no folder under user/wii/title yet), no matter which game it is.
Existing games and savegames are not affected, but I cannot create saves for new games. I can create them but then dolphin crashes at next startup during game folder scanning. Every new savegame folder wihich is created seems to cause dolphin to crash until the game or the savegame is deleted. Deleting another game or savegame will not help, it must be exatly the one that caused the crash. However the new savegame can be migrated to another Dolphin installation without any problems.

There are currently 173 existing folders under /user/wii/title which seem to work fine. But every new folder created by a game causes a crash at dolphin startup when scanning the new game files.

No, there was no message like that. There seems to a limitation on how many NAND files dolphin can scan at startup.
If I move the save to a brand new installation which is not using the same NAND root folder, dolphin starts fine and shows the banner of the game causing the crash in other installations. In my opinion, just the scanning at dolphin startup needs to be fixed to allow more nand entrys to be scanned. So the crash could be prevented.

There seems to be a maximum of 109 files with corresponding nand entrys in the game folder that dolphin can handle.
If I just create a 110th game file with an existing NAND entry (by duplicating an existing file), dolphin will crash at startup.
If I create a new 110th game file which has no NAND entry yet, dolphin will not crash at startup until I create a savegame.

Maybe there is a maximum number of savegames also. If i remove existing games and savegame folders from the game folder and create a new savegame, it still crashes.
According to Wii system menu, there are 580 open blocks. Deleting existing savegames from wii system menu will not stop dolphin from crashing.

However, I can migrate saves, even new saves to another wii NAND where they will run fine.

I tried to reproduce the crash with a clean installation by duplicating a game file with an existing savegame 120 times -> no crash so far

Interestingly, if I manage to ensure a stable startup behavior by deleting savegames causing the crash dolphin runs stable until a new additional save folder under user/wii/title is created. But if I delete the entire content of user/cache then dolphin crashes immediately at next startup on every single wii file and savegame beginning with 0, A...
It crashes after removing the cache even if the exact same installation starts normally with cache files in place.

So the problem seems to be located within the cache folder...
Whenever a new wii cache file is being created on dolphin startup, dolphin crashes.

If I the copy the cache file causing the error from another, currently working dolphin installation using the same nand root, dolphin works again, with no problems until a new cache file is being created at startup.

I do not think it is a save block limit, since there are more than 500 blocks left. But maybe when scanning the game files, save files and cache files at startup there is some kind of overflow where some numbers run out of their given limits.

It only happens when creating a cache file for a game present in the game folder that already has a save present in the save folder. If the game file or the save file ore both are deleted or if the cache files are copied from another installation and do not have to be created no crash will happen.

The crash may only happen if a large numer of games and saves are present. But if it happened once it will always happen even if the overall numer of games or saves is reduced.

Even if I copy the NAND folder to a new installation, the crash will still happen.

Update: If I only copy the title folder instead of the whole user/wii folder to a new installation everything seems to work fine.

Update2: Now I have 3 different 3.0-735 installations using the same freshly created NAND folder with my old title save files. All 3 use the same configuration and same game folders. The two old 3.0-735 installations have the above bug. But the new Lectrode 3.0-735 build does not crash.

All below installations use the same settings and share exactly the same wii nand folder:
After unzipping a brand new installation I just set the nand folder and the game folder to my common settings: